2CO0

WDR5 and unmodified Histone H3 complex at 2.25 angstrom


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Histone H3 Recognition and Presentation by the Wdr5 Module of the Mll1 Complex

Ruthenburg, A.J.Wang, W.Graybosch, D.M.Li, H.Allis, C.D.Patel, D.J.Verdine, G.L.

(2006) Nat.Struct.Mol.Biol. 13: 704

  • DOI: 10.1038/nsmb1119
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • WDR5 is a core component of SET1-family complexes that achieve transcriptional activation via methylation of histone H3 on Nzeta of Lys4 (H3K4). The role of WDR5 in the MLL1 complex has recently been described as specific recognition of dimethyl-K4 i ...

    WDR5 is a core component of SET1-family complexes that achieve transcriptional activation via methylation of histone H3 on Nzeta of Lys4 (H3K4). The role of WDR5 in the MLL1 complex has recently been described as specific recognition of dimethyl-K4 in the context of a histone H3 amino terminus; WDR5 is essential for vertebrate development, Hox gene activation and global H3K4 trimethylation. We report the high-resolution X-ray structures of WDR5 in the unliganded form and complexed with histone H3 peptides having unmodified and mono-, di- and trimethylated K4, which together provide the first comprehensive analysis of methylated histone recognition by the ubiquitous WD40-repeat fold. Contrary to predictions, the structures reveal that WDR5 does not read out the methylation state of K4 directly, but instead serves to present the K4 side chain for further methylation by SET1-family complexes.


    Organizational Affiliation

    Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
WD-REPEAT PROTEIN 5
A
315Homo sapiensMutation(s): 0 
Gene Names: WDR5 (BIG3)
Find proteins for P61964 (Homo sapiens)
Go to Gene View: WDR5
Go to UniProtKB:  P61964
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
HISTONE H3 DIMETHYL-LYSINE 4
B, D
15Homo sapiensMutation(s): 0 
Gene Names: HIST1H3A, HIST1H3B, HIST1H3C, HIST1H3D, HIST1H3E, HIST1H3F, HIST1H3G, HIST1H3H, HIST1H3I, HIST1H3J (H3FA, H3FL, H3FC, H3FB, H3FD, H3FI, H3FH, H3FK, H3FF, H3FJ)
Find proteins for P68431 (Homo sapiens)
Go to UniProtKB:  P68431
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
WD-REPEAT PROTEIN 5
C
315Homo sapiensMutation(s): 0 
Gene Names: WDR5 (BIG3)
Find proteins for P61964 (Homo sapiens)
Go to Gene View: WDR5
Go to UniProtKB:  P61964
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.190 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 64.916α = 90.00
b = 47.030β = 107.01
c = 101.768γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PHASERphasing
CNSrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-07-03
    Type: Initial release
  • Version 1.1: 2016-12-21
    Type: Data collection, Database references, Derived calculations, Non-polymer description, Other, Source and taxonomy, Structure summary, Version format compliance
  • Version 1.2: 2018-04-04
    Type: Data collection